1
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Wackett LP. Microwell fluoride assay screening for enzymatic defluorination. Methods Enzymol 2024; 696:65-83. [PMID: 38658089 DOI: 10.1016/bs.mie.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
There is intense interest in removing fluorinated compounds from the environment, environments are most efficiently remediated by microbial enzymes, and defluorinating enzymes are readily monitored by fluoride determination. Fluorine is the most electronegative element. Consequently, all mechanisms of enzymatic C-F bond cleavage produce fluoride anion, F-. Therefore, methods for the determination of fluoride are critical for C-F enzymology and apply to any fluorinated organic compounds, including PFAS, or per- and polyfluorinated alkyl substances. The biodegradation of most PFAS chemicals is rare or unknown. Accordingly, identifying new enzymes, or re-engineering the known defluorinases, will require rapid and sensitive methods for measuring fluoride in aqueous media. Most studies currently use ion chromatography or fluoride specific electrodes which are relatively sensitive but low throughput. The methods here describe refashioning a drinking water test to efficiently determine fluoride in enzyme and cell culture reaction mixtures. The method is based on lanthanum alizarin complexone binding of fluoride. Reworking the method to a microtiter well plate format allows detection of as little as 4 nmol of fluoride in 200 μL of assay buffer. The method is amenable to color imaging, spectrophotometric plate reading and automated liquid handling to expedite assays with thousands of enzymes and/or substrates for discovering and improving enzymatic defluorination.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, United States.
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2
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Firsova YE, Torgonskaya ML. Different roles of two groEL homologues in methylotrophic utiliser of dichloromethane Methylorubrum extorquens DM4. Antonie van Leeuwenhoek 2019; 113:101-116. [PMID: 31463590 DOI: 10.1007/s10482-019-01320-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/19/2019] [Indexed: 11/28/2022]
Abstract
The genome of methylotrophic bacteria Methylorubrum extorquens DM4 contains two homologous groESL operons encoding the 60-kDa and 10-kDa subunits of GroE heat shock chaperones with highly similar amino acid sequences. To test a possible functional redundancy of corresponding GroEL proteins we attempted to disrupt the groEL1 and groEL2 genes. Despite the large number of recombinants analysed and the gentle culture conditions the groEL1-lacking mutant was not constructed suggesting that the loss of GroEL1 was lethal for cells. At the same time the ∆groEL2 strain was viable and varied from the wild-type by increased sensitivity to acid, salt and desiccation stresses as well as by the impaired growth with a toxic halogenated compound-dichloromethane (DCM). The evaluation of activity of putative PgroE1 and PgroE2 promoters using the reporter gene of green fluorescent protein (GFP) showed that the expression of groESL1 operon greatly prevails (about two orders of magnitude) over those of groESL2 under all tested conditions. However the above promoters demonstrated differential regulation in response to stresses. The expression from PgroE1 was heat-inducible, while the activity of PgroE2 was upregulated upon acid shock and cultivation with DCM. Based on these results we conclude that the highly conservative groESL1 operon (old locus tags METDI5839-5840) encodes the housekeeping chaperone essential for fundamental cellular processes. On the contrary the second pair of paralogues (METDI4129-4130) is dispensable, but corresponding GroE2 chaperone promotes the tolerance to acid and salt stresses, in particular, during the growth with DCM.
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Affiliation(s)
- Yulia E Firsova
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Maria L Torgonskaya
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, Pushchino, Russia, 142290.
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3
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Torgonskaya ML, Zyakun AM, Trotsenko YA, Laurinavichius KS, Kümmel S, Vuilleumier S, Richnow HH. Individual stages of bacterial dichloromethane degradation mapped by carbon and chlorine stable isotope analysis. J Environ Sci (China) 2019; 78:147-160. [PMID: 30665634 DOI: 10.1016/j.jes.2018.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 07/20/2018] [Accepted: 09/12/2018] [Indexed: 06/09/2023]
Abstract
The fractionation of carbon and chlorine stable isotopes of dichloromethane (CH2Cl2, DCM) upon dechlorination by cells of the aerobic methylotroph Methylobacterium extorquens DM4 and by purified DCM dehalogenases of the glutathione S-transferase family was analyzed. Isotope effects for individual steps of the multi-stage DCM degradation process, including transfer across the cell wall from the aqueous medium to the cell cytoplasm, dehalogenase binding, and catalytic reaction, were considered. The observed carbon and chlorine isotope fractionation accompanying DCM consumption by cell supensions and enzymes was mainly determined by the breaking of CCl bonds, and not by inflow of DCM into cells. Chlorine isotope effects of DCM dehalogenation were initially masked in high density cultures, presumably due to inverse isotope effects of non-specific DCM oxidation under conditions of oxygen excess. Glutathione cofactor supply remarkably affected the correlation of variations of DCM carbon and chlorine stable isotopes (Δδ13C/Δδ37Cl), increasing corresponding ratio from 7.2-8.6 to 9.6-10.5 under conditions of glutathione deficiency. This suggests that enzymatic reaction of DCM with glutathione thiolate may involve stepwise breaking and making of bonds with the carbon atom of DCM, unlike the uncatalyzed reaction, which is a one-stage process, as shown by quantum-chemical modeling.
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Affiliation(s)
- Maria L Torgonskaya
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research, Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Anatoly M Zyakun
- Laboratory of Mass Spectrometry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Yuri A Trotsenko
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Kestutis S Laurinavichius
- Laboratory of Mass Spectrometry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | | | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
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Smirnov SV, Demin OV, Torgonskaya ML, Firsova YE, Zhukov VG, Zagustina NA. Optimization of the Process of Air Purification from Dichloromethane in a Biofilter with an Irrigated Layer by Mathematical Modeling. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818060121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Hermon L, Denonfoux J, Hellal J, Joulian C, Ferreira S, Vuilleumier S, Imfeld G. Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses. WATER RESEARCH 2018; 142:217-226. [PMID: 29885622 DOI: 10.1016/j.watres.2018.05.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/25/2018] [Accepted: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Dichloromethane (DCM) is a widespread and toxic industrial solvent which often co-occurs with chlorinated ethenes at polluted sites. Biodegradation of DCM occurs under both oxic and anoxic conditions in soils and aquifers. Here we investigated in situ and ex situ biodegradation of DCM in groundwater sampled from the industrial site of Themeroil (France), where DCM occurs as a major co-contaminant of chloroethenes. Carbon isotopic fractionation (εC) for DCM ranging from -46 to -22‰ were obtained under oxic or denitrifying conditions, in mineral medium or contaminated groundwater, and for laboratory cultures of Hyphomicrobium sp. strain GJ21 and two new DCM-degrading strains isolated from the contaminated groundwater. The extent of DCM biodegradation (B%) in the aquifer, as evaluated by compound-specific isotope analysis (δ13C), ranged from 1% to 85% applying DCM-specific εC derived from reference strains and those determined in this study. Laboratory groundwater microcosms under oxic conditions showed DCM biodegradation rates of up to 0.1 mM·day-1, with concomitant chloride release. Dehalogenase genes dcmA and dhlA involved in DCM biodegradation ranged from below 4 × 102 (boundary) to 1 × 107 (source zone) copies L-1 across the contamination plume. High-throughput sequencing on the 16S rrnA gene in groundwater samples showed that both contaminant level and terminal electron acceptor processes (TEAPs) influenced the distribution of genus-level taxa associated with DCM biodegradation. Taken together, our results demonstrate the potential of DCM biodegradation in multi-contaminated groundwater. This integrative approach may be applied to contaminated aquifers in the future, in order to identify microbial taxa and pathways associated with DCM biodegradation in relation to redox conditions and co-contamination levels.
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Affiliation(s)
- L Hermon
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France; BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - J Denonfoux
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen Lille, France
| | - J Hellal
- BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - C Joulian
- BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - S Ferreira
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen Lille, France
| | - S Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - G Imfeld
- Université de Strasbourg, CNRS/EOST, LHyGeS UMR 7517, Laboratory of Hydrology and Geochemistry of Strasbourg, Strasbourg, France.
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Firsova YE, Torgonskaya ML, Trotsenko YA. Functionality of Metdi5511gene in Methylobacterium dichloromethanicum DM4. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Firsova YE, Torgonskaya ML, Trotsenko YA. Functionality of the xoxF gene in Methylobacterium dichloromethanicum DM4. Microbiology (Reading) 2015. [DOI: 10.1134/s002626171506003x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Nadalig T, Greule M, Bringel F, Keppler F, Vuilleumier S. Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation. Front Microbiol 2014; 5:523. [PMID: 25360131 PMCID: PMC4197683 DOI: 10.3389/fmicb.2014.00523] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/19/2014] [Indexed: 11/13/2022] Open
Abstract
Chloromethane (CH3Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH3Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH3Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH3Cl. The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH3Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH3Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH3Cl contain part or all of the complement of cmu genes required for CH3Cl degradation. These organisms, unlike bacteria shown to grow with CH3Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans MB2 showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans MB2 suggest that the unknown pathway used by this bacterium for growth with CH3Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH3Cl budget may be teased apart in the future.
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Affiliation(s)
- Thierry Nadalig
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
| | - Markus Greule
- Institute of Earth Sciences, Ruprecht Karls University Heidelberg Heidelberg, Germany
| | - Françoise Bringel
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Ruprecht Karls University Heidelberg Heidelberg, Germany
| | - Stéphane Vuilleumier
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
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9
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Phylogeny poorly predicts the utility of a challenging horizontally transferred gene in Methylobacterium strains. J Bacteriol 2014; 196:2101-7. [PMID: 24682326 DOI: 10.1128/jb.00034-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Horizontal gene transfer plays a crucial role in microbial evolution. While much is known about the mechanisms that determine whether physical DNA can be transferred into a new host, the factors determining the utility of the transferred genes are less clear. We have explored this issue using dichloromethane consumption in Methylobacterium strains. Methylobacterium extorquens DM4 expresses a dichloromethane dehalogenase (DcmA) that has been acquired through horizontal gene transfer and allows the strain to grow on dichloromethane as the sole carbon and energy source. We transferred the dcmA gene into six Methylobacterium strains that include both close and distant evolutionary relatives. The transconjugants varied in their ability to grow on dichloromethane, but their fitness on dichloromethane did not correlate with the phylogeny of the parental strains or with any single tested physiological factor. This work highlights an important limiting factor in horizontal gene transfer, namely, the capacity of the recipient strain to accommodate the stress and metabolic disruption resulting from the acquisition of a new enzyme or pathway. Understanding these limitations may help to rationalize historical examples of horizontal transfer and aid deliberate genetic transfers in biotechnology for metabolic engineering.
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Penketh PG, Shyam K, Zhu R, Baumann RP, Ishiguro K, Sartorelli AC. Influence of phosphate and phosphoesters on the decomposition pathway of 1,2-bis(methylsulfonyl)-1-(2-chloroethyhydrazine (90CE), the active anticancer moiety generated by Laromustine, KS119, and KS119W. Chem Res Toxicol 2014; 27:818-33. [PMID: 24618018 PMCID: PMC4033638 DOI: 10.1021/tx500004y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Prodrugs of the short-lived chloroethylating
agent 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)hydrazine
(90CE) and its methylating analogue 1,2-bis(methylsulfonyl)-1-(methyl)hydrazine
(KS90) are potentially useful anticancer agents. This class of agents
frequently yields higher ratios of therapeutically active oxophilic
electrophiles responsible for DNA O6-guanine
alkylations to other electrophiles with lower therapeutic relevance
than the nitrosoureas. This results in improved selectivity toward
tumors with diminished levels of O6-alkylguanine-DNA
alkyltransferase (MGMT), the resistance protein responsible for O6-alkylguanine repair. The formation of O6-(2-chloroethyl)guanine, which leads to the
formation of a DNA–DNA interstrand cross-link, accounts for
the bulk of the anticancer activity of 90CE prodrugs. Herein, we describe
a new decomposition pathway that is available to 90CE but not to its
methylating counterpart. This pathway appears to be subject to general/acid
base catalysis with phosphate (Pi), phosphomonoesters, and phosphodiesters,
being particularly effective. This pathway does not yield a chloroethylating
species and results in a major change in nucleophile preference since
thiophilic rather than oxophilic electrophiles are produced. Thus,
a Pi concentration dependent decrease in DNA–DNA interstand
cross-link formation was observed. Changes in 90CE decomposition products
but not alkylation kinetics occurred in the presence of Pi since the
prebranch point elimination of the N-1 methanesulfinate moiety remained
the rate-limiting step. The Pi catalyzed route is expected to dominate
at Pi and phosphoester concentrations totaling >25–35 mM.
In
view of the abundance of Pi and phosphoesters in cells, this pathway
may have important effects on agent toxicity, tumor selectivity, and
resistance to prodrugs of 90CE. Furthermore, it may be possible to
design analogues that diminish this thiophile-generating pathway,
which is likely superfluous at best and potentially detrimental to
the targeting of hypoxic regions where Pi concentrations can be significantly
elevated.
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Affiliation(s)
- Philip G Penketh
- Department of Pharmacology and Yale Cancer Center, Yale University School of Medicine , 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
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Nadalig T, Greule M, Bringel F, Vuilleumier S, Keppler F. Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria. Microbiologyopen 2013; 2:893-900. [PMID: 24019296 PMCID: PMC3892336 DOI: 10.1002/mbo3.124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/10/2013] [Accepted: 07/21/2013] [Indexed: 01/12/2023] Open
Abstract
Chloromethane (CH3 Cl) is a widely studied volatile halocarbon involved in the destruction of ozone in the stratosphere. Nevertheless, its global budget still remains debated. Stable isotope analysis is a powerful tool to constrain fluxes of chloromethane between various environmental compartments which involve a multiplicity of sources and sinks, and both biotic and abiotic processes. In this study, we measured hydrogen and carbon isotope fractionation of the remaining untransformed chloromethane following its degradation by methylotrophic bacterial strains Methylobacterium extorquens CM4 and Hyphomicrobium sp. MC1, which belong to different genera but both use the cmu pathway, the only pathway for bacterial degradation of chloromethane characterized so far. Hydrogen isotope fractionation for degradation of chloromethane was determined for the first time, and yielded enrichment factors (ε) of -29‰ and -27‰ for strains CM4 and MC1, respectively. In agreement with previous studies, enrichment in (13) C of untransformed CH3 Cl was also observed, and similar isotope enrichment factors (ε) of -41‰ and -38‰ were obtained for degradation of chloromethane by strains CM4 and MC1, respectively. These combined hydrogen and carbon isotopic data for bacterial degradation of chloromethane will contribute to refine models of the global atmospheric budget of chloromethane.
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Affiliation(s)
- Thierry Nadalig
- Equipe Adaptations et Interactions Microbiennes dans l'Environnement, UMR 7156 Université de Strasbourg - CNRS, 28 rue Goethe, Strasbourg, 67083, France
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12
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Fluorescence-based bacterial bioreporter for specific detection of methyl halide emissions in the environment. Appl Environ Microbiol 2013; 79:6561-7. [PMID: 23956392 DOI: 10.1128/aem.01738-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Methyl halides are volatile one-carbon compounds responsible for substantial depletion of stratospheric ozone. Among them, chloromethane (CH3Cl) is the most abundant halogenated hydrocarbon in the atmosphere. Global budgets of methyl halides in the environment are still poorly understood due to uncertainties in their natural sources, mainly from vegetation, and their sinks, which include chloromethane-degrading bacteria. A bacterial bioreporter for the detection of methyl halides was developed on the basis of detailed knowledge of the physiology and genetics of Methylobacterium extorquens CM4, an aerobic alphaproteobacterium which utilizes chloromethane as the sole source of carbon and energy. A plasmid construct with the promoter region of the chloromethane dehalogenase gene cmuA fused to a promotorless yellow fluorescent protein gene cassette resulted in specific methyl halide-dependent fluorescence when introduced into M. extorquens CM4. The bacterial whole-cell bioreporter allowed detection of methyl halides at femtomolar levels and quantification at concentrations above 10 pM (approximately 240 ppt). As shown for the model chloromethane-producing plant Arabidopsis thaliana in particular, the bioreporter may provide an attractive alternative to analytical chemical methods to screen for natural sources of methyl halide emissions.
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Plekhanova YV, Firsova YE, Doronina NV, Trotsenko YA, Reshetilov AN. Aerobic methylobacteria as the basis for a biosensor for dichloromethane detection. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683813020130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Firsova YE, Fedorov DN, Trotsenko YA. Functional analysis of the genome fragment involved in aerobic dichloromethane degradation by Methylobacterium dichloromethanicum DM4. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812050043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Firsova YE, Fedorov DN, Trotsenko YA. Analysis of the 3′-region of the dcmA gene of dichloromethane dehalogenase of Methylobacterium dichloromethanicum DM4. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711060075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Nadalig T, Farhan Ul Haque M, Roselli S, Schaller H, Bringel F, Vuilleumier S. Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilization genes. FEMS Microbiol Ecol 2011; 77:438-48. [PMID: 21545604 DOI: 10.1111/j.1574-6941.2011.01125.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Chloromethane gas is produced naturally in the phyllosphere, the compartment defined as the aboveground parts of vegetation, which hosts a rich bacterial flora. Chloromethane may serve as a growth substrate for specialized aerobic methylotrophic bacteria, which have been isolated from soil and water environments, and use cmu genes for chloromethane utilization. Evidence for the presence of chloromethane-degrading bacteria on the leaf surfaces of Arabidopsis thaliana was obtained by specific quantitative PCR of the cmuA gene encoding the two-domain methyltransferase corrinoid protein of chloromethane dehalogenase. Bacterial strains were isolated on a solid mineral medium with chloromethane as the sole carbon source from liquid mineral medium enrichment cultures inoculated with leaves of A. thaliana. Restriction analysis-based genotyping of cmuA PCR products was used to evaluate the diversity of chloromethane-degrading bacteria during enrichment and after strain isolation. The isolates obtained, affiliated to the genus Hyphomicrobium based on their 16S rRNA gene sequence and the presence of characteristic hyphae, dehalogenate chloromethane, and grow in a liquid culture with chloromethane as the sole carbon and energy source. The cmu genes of these isolates were analysed using new PCR primers, and their sequences were compared with those of previously reported aerobic chloromethane-degrading strains. The three isolates featured a colinear cmuBCA gene arrangement similar to that of all previously characterized strains, except Methylobacterium extorquens CM4 of known genome sequence.
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Affiliation(s)
- Thierry Nadalig
- Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France.
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17
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Torgonskaya ML, Doronina NV, Hourcade E, Trotsenko YA, Vuilleumier S. Chloride-associated adaptive response in aerobic methylotrophic dichloromethane-utilising bacteria. J Basic Microbiol 2011; 51:296-303. [PMID: 21298685 DOI: 10.1002/jobm.201000280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Accepted: 10/07/2010] [Indexed: 11/10/2022]
Abstract
Aerobic methylotrophic bacteria able to grow with dichloromethane (DCM) as the sole carbon and energy source possess a specific glutathione S-transferase, DCM dehalogenase, which transforms DCM to formaldehyde, used for biomass and energy production, and hydrochloric acid, which is excreted. Evidence is presented for chloride-specific responses for three DCM-degrading bacteria, Methylobacterium extorquens DM4, Methylopila helvetica DM6 and Albibacter methylovorans DM10. Chloride release into the medium was inhibited by sodium azide and m -chlorophenylhydrazone, suggesting an energy-dependent process. In contrast, only nigericin affected chloride excretion in Mb. extorquens DM4 and Mp. helvetica DM6, while valinomycin had the same effect in A. methylovorans DM10 only. Chloride ions stimulated DCM-dependent induction of DCM dehalogenase expression for Mp. helvetica DM6 and A. methylovorans DM10, and shortened the time for onset of chloride release into the medium. Striking chloride-containing structures were observed by electron microscopy and X-ray microanalysis on the cell surface of Mp. helvetica DM6 and A. methylovorans DM10 during growth with DCM, and with methanol in medium supplemented with sodium chloride. Taken together, these data suggest the existence of both general and specific chloride-associated adaptations in aerobic DCM-degrading bacteria.
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Affiliation(s)
- Maria L Torgonskaya
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Science Avenue, Pushchino, Moscow region, 142290, Russia
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18
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Painter RG, Marrero L, Lombard GA, Valentine VG, Nauseef WM, Wang G. CFTR-mediated halide transport in phagosomes of human neutrophils. J Leukoc Biol 2010; 87:933-42. [PMID: 20089668 DOI: 10.1189/jlb.1009655] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Chloride serves as a critical component of innate host defense against infection, providing the substrate for MPO-catalyzed production of HOCl in the phagosome of human neutrophils. Here, we used halide-specific fluorescent sensors covalently coupled to zymosan particles to investigate the kinetics of chloride and iodide transport in phagosomes of human neutrophils. Using the self-ratioable fluorescent probe specific for chloride anion, we measured chloride dynamics within phagosomes in response to extracellular chloride changes by quantitative fluorescence microscopy. Under the experimental conditions used, normal neutrophils showed rapid phagosomal chloride uptake with an initial influx rate of 0.31 +/- 0.04 mM/s (n=5). GlyH-101, a CFTR(inh), decreased the rate of uptake in a dose-dependent manner. Neutrophils isolated from CF patients showed a significantly slower rate of chloride uptake by phagosomes, having an initial influx rate of 0.043 +/- 0.012 mM/s (n=5). Interestingly, the steady-state level of chloride in CF phagosomes was approximately 26 mM, significantly lower than that of the control ( approximately 68 mM). As CFTR transports chloride as well as other halides, we conjugated an iodide-sensitive probe as an independent approach to confirm the results. The dynamics of iodide uptake by neutrophil phagosomes were monitored by flow cytometry. CFTR(inh)172 blocked 40-50% of the overall iodide uptake by phagosomes in normal neutrophils. In a parallel manner, the level of iodide uptake by CF phagosomes was only 20-30% of that of the control. Taken together, these results implicate CFTR in transporting halides into the phagosomal lumen.
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Affiliation(s)
- Richard G Painter
- Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA
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Chen JW, Yang CS, Ren FL, Xiao JB, Xu M. Highly sensitive determination of chloride ions in serum using a Rayleigh light scattering technique. MEASUREMENT SCIENCE AND TECHNOLOGY 2007. [DOI: 10.1088/0957-0233/18/7/034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Feske BD, Kaluzna IA, Stewart JD. Enantiodivergent, biocatalytic routes to both taxol side chain antipodes. J Org Chem 2006; 70:9654-7. [PMID: 16268655 DOI: 10.1021/jo0516077] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[Reaction: see text]. Two enantiocomplementary bakers' yeast enzymes reduced an alpha-chloro-beta-keto ester to yield precursors for both enantiomers of the N-benzoyl phenylisoserine Taxol side chain. After base-mediated ring closure of the chlorohydrin enantiomers, the epoxides were converted directly to the oxazoline form of the target molecules using a Ritter reaction with benzonitrile. These were hydrolyzed to the ethyl ester form of the Taxol side chain enantiomers under acidic conditions. This brief and atom-efficient route to both target enantiomers demonstrates both the synthetic utility of individual yeast reductases and the power of genomic strategies in making these catalysts available.
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Affiliation(s)
- Brent D Feske
- Department of Chemistry, University of Florida, 127 Chemistry Research Building, Gainesville, Florida 32611, USA
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